NM_001387691.1:c.7C>T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001387691.1(POM121):c.7C>T(p.Pro3Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000318 in 1,430,538 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001387691.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POM121 | NM_001387691.1 | c.7C>T | p.Pro3Ser | missense_variant | Exon 1 of 13 | ENST00000434423.5 | NP_001374620.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POM121 | ENST00000434423.5 | c.7C>T | p.Pro3Ser | missense_variant | Exon 1 of 13 | 5 | NM_001387691.1 | ENSP00000405562.2 | ||
POM121 | ENST00000395270.5 | c.-151-1134C>T | intron_variant | Intron 4 of 15 | 1 | ENSP00000378687.1 | ||||
POM121 | ENST00000627934.3 | c.-151-1134C>T | intron_variant | Intron 3 of 14 | 5 | ENSP00000486504.1 | ||||
ENSG00000272843 | ENST00000608799.1 | n.-3G>A | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 103AN: 152120Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00287 AC: 90AN: 31354Hom.: 3 AF XY: 0.00210 AC XY: 39AN XY: 18590
GnomAD4 exome AF: 0.000275 AC: 352AN: 1278302Hom.: 8 Cov.: 30 AF XY: 0.000268 AC XY: 168AN XY: 627954
GnomAD4 genome AF: 0.000677 AC: 103AN: 152236Hom.: 1 Cov.: 32 AF XY: 0.000766 AC XY: 57AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
POM121: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at